Supercomputers can be used to simulate chemical reactions, saving time and money and increasing safety.

Chemical
Experiments and Predictions by Computer

The term “chemistry” conjures
up images of people in white lab coats, pouring liquids from test tubes
into a beaker. But an increasing number of chemists do most of their chemistry
on computers, partly to save money and increase safety. Simulating chemistry
experiments on the computer instead of doing them in the lab can produce
chemical reactions and properties with a faster turnaround and better
accuracy. Computational chemistry also can aid understanding of actual
lab results.

David Bernholdt, who helped
develop the NWChem computational chemistry software package while a postdoctoral
scientist at DOE’s Pacific Northwest National Laboratory, leads the chemistry
initiative at DOE’s Center for Computational Sciences at ORNL. Bernholdt
knows the value of computational chemistry, so he is working to develop
scaling techniques that will allow chemists to work with even larger molecules
on ORNL’s new supercomputers.

Snapshot
of a droplet of water (red and white), too small to be seen, which
has formed spontaneously in carbon dioxide (invisible for clarity)
and is stabilized by a novel surfactant (blue and turquoise). The
size of the droplet formed in the simulation agreed with experimental
measurements.

“Computational chemistry allows
you to predict which chemical compounds are more likely to give the desired
property or result,” he says. “For instance, computational chemistry was
used by Kodak’s color film developers to predict which chemicals would
produce the right colors yet still hold up during chemical processing
to develop the film. It saves you from having to synthesize lots of different
chemicals and then screen them for the needed properties, such as what
might be effective in a therapeutic drug.”

At ORNL several researchers
have been using supercomputers to work on computational chemistry projects.
Don Noid and Bobby Sumpter, both in ORNL’s Computer Science and Mathematics
Division, were the first to computationally model the dynamics of fluid
flow inside carbon nanotubestiny cylinders resembling rolled-up
chicken wire. Their molecular dynamics simulations showed that argon slowed
down more quickly than helium and that both fluids slowed down faster
in a flexible nanotube than in a rigid one.

More recently, they found
in their simulation studies with Clemson University researchers that hydrocarbons
break up more slowly when heated in carbon nanotubes than in a furnace
under vacuum. They believe the rate of breakup of these polymers (similar
to crude oil cracking under pyrolysis) is altered by the chemistry of
confined spaces.

Working with Mike Barnes of
ORNL’s Chemical Sciences Division (CSD), Noid and Sumpter showed both
computationally and experimentally that a nanosized polymer droplet can
be formed from materials that don’t normally mix and that the droplet
can be forced through a micron-sized orifice. The resulting particles
exhibit unique properties that could make them useful for optical displays
and industrial coatings. The researchers also helped develop a software
tool to calculate how far and which way thousands of atoms move relative
to their neighbors (vibrational modes), providing insight into the structure
and behavior of various materials.

Hank Cochran, Peter Cummings, and
Shengting Cui, all with both CSD and the University of Tennessee at Knoxville,
are doing molecular simulations of microdispersions stabilized by surfactants
in supercritical carbon dioxide (CO2). Surfactants act like
detergent by reducing surface tension; they are being used in several
new dry cleaning establishments where CO2 replaces traditionally
used carcinogenic solvents. DuPont is building a big plant in North Carolina
to produce Teflon and other fluoryl polymers using other new surfactants
with supercritical CO2 instead of ozone-destroying chlorinated
fluorocarbons.

Solid-like
structure (with short-range order in three dimensions) of n-dodecane
narrowly confined between solid surfaces is induced by interfacial
forces. This effect may explain the orders-of-magnitude higher viscosity
observed in confined-fluid experiments compared with bulk fluid values.

The CSD group is also simulating
the effects of velocity gradients (shear flow) on the arrangement and
behavior of long-chain molecules in such situations as during the extrusion
of filaments and the melting of polymers. In addition, they are looking
at the behavior of lubricants in the narrowest nanoscale separations between
motor vehicle components, which can be substantially different from their
behavior in bulk.

Cochran and Cui are simulating
the behavior of water that contains salts and DNA or proteins in channels
thousands of times smaller than a hair in a “nanofluidic lab on a chip.”
When developed, under the leadership of lab-on-a-chip inventor Mike Ramsey
of CSD, such a device might be used in a doctor’s office for ultrafast
DNA sequencing of blood drops from individual patients for rapid disease
diagnosis. Liquids containing DNA or protein could be moved by the influence
of electric fields through ultrasmall channels, which might enable the
increase of sequencing and diagnostic speeds by a million to a billion
times. In their simulations, the researchers take into account the electric-field
and surface forces that extend through the liquid inside the nanoscale
channel. These simulations help to guide and interpret Ramsey’s experiments.

As devices get smaller, computational
chemistry is likely to play a bigger role in figuring out how to make
them work.